48 research outputs found
Reasoning with Uncertainty in Deep Learning for Safer Medical Image Computing
Deep learning is now ubiquitous in the research field of medical image computing. As such technologies progress towards clinical translation, the question of safety becomes critical. Once deployed, machine learning systems unavoidably face situations where the correct decision or prediction is ambiguous. However, the current methods disproportionately rely on deterministic algorithms, lacking a mechanism to represent and manipulate uncertainty. In safety-critical applications such as medical imaging, reasoning under uncertainty is crucial for developing a reliable decision making system. Probabilistic machine learning provides a natural framework to quantify the degree of uncertainty over different variables of interest, be it the prediction, the model parameters and structures, or the underlying data (images and labels). Probability distributions are used to represent all the uncertain unobserved quantities in a model and how they relate to the data, and probability theory is used as a language to compute and manipulate these distributions. In this thesis, we explore probabilistic modelling as a framework to integrate uncertainty information into deep learning models, and demonstrate its utility in various high-dimensional medical imaging applications. In the process, we make several fundamental enhancements to current methods. We categorise our contributions into three groups according to the types of uncertainties being modelled: (i) predictive; (ii) structural and (iii) human uncertainty. Firstly, we discuss the importance of quantifying predictive uncertainty and understanding its sources for developing a risk-averse and transparent medical image enhancement application. We demonstrate how a measure of predictive uncertainty can be used as a proxy for the predictive accuracy in the absence of ground-truths. Furthermore, assuming the structure of the model is flexible enough for the task, we introduce a way to decompose the predictive uncertainty into its orthogonal sources i.e. aleatoric and parameter uncertainty. We show the potential utility of such decoupling in providing a quantitative “explanations” into the model performance. Secondly, we introduce our recent attempts at learning model structures directly from data. One work proposes a method based on variational inference to learn a posterior distribution over connectivity structures within a neural network architecture for multi-task learning, and share some preliminary results in the MR-only radiotherapy planning application. Another work explores how the training algorithm of decision trees could be extended to grow the architecture of a neural network to adapt to the given availability of data and the complexity of the task. Lastly, we develop methods to model the “measurement noise” (e.g., biases and skill levels) of human annotators, and integrate this information into the learning process of the neural network classifier. In particular, we show that explicitly modelling the uncertainty involved in the annotation process not only leads to an improvement in robustness to label noise, but also yields useful insights into the patterns of errors that characterise individual experts
Deeper Image Quality Transfer: Training Low-Memory Neural Networks for 3D Images
In this paper we address the memory demands that come with the processing of
3-dimensional, high-resolution, multi-channeled medical images in deep
learning. We exploit memory-efficient backpropagation techniques, to reduce the
memory complexity of network training from being linear in the network's depth,
to being roughly constant permitting us to elongate deep architectures
with negligible memory increase. We evaluate our methodology in the paradigm of
Image Quality Transfer, whilst noting its potential application to various
tasks that use deep learning. We study the impact of depth on accuracy and show
that deeper models have more predictive power, which may exploit larger
training sets. We obtain substantially better results than the previous
state-of-the-art model with a slight memory increase, reducing the
root-mean-squared-error by . Our code is publicly available.Comment: Accepted in: MICCAI 201
An Image is Worth Multiple Words: Learning Object Level Concepts using Multi-Concept Prompt Learning
Textural Inversion, a prompt learning method, learns a singular embedding for
a new "word" to represent image style and appearance, allowing it to be
integrated into natural language sentences to generate novel synthesised
images. However, identifying and integrating multiple object-level concepts
within one scene poses significant challenges even when embeddings for
individual concepts are attainable. This is further confirmed by our empirical
tests. To address this challenge, we introduce a framework for Multi-Concept
Prompt Learning (MCPL), where multiple new "words" are simultaneously learned
from a single sentence-image pair. To enhance the accuracy of word-concept
correlation, we propose three regularisation techniques: Attention Masking
(AttnMask) to concentrate learning on relevant areas; Prompts Contrastive Loss
(PromptCL) to separate the embeddings of different concepts; and Bind adjective
(Bind adj.) to associate new "words" with known words. We evaluate via image
generation, editing, and attention visualisation with diverse images. Extensive
quantitative comparisons demonstrate that our method can learn more
semantically disentangled concepts with enhanced word-concept correlation.
Additionally, we introduce a novel dataset and evaluation protocol tailored for
this new task of learning object-level concepts.Comment: Project page: https://github.com/lxasqjc/MCP
Learning From Noisy Labels By Regularized Estimation Of Annotator Confusion
The predictive performance of supervised learning algorithms depends on the
quality of labels. In a typical label collection process, multiple annotators
provide subjective noisy estimates of the "truth" under the influence of their
varying skill-levels and biases. Blindly treating these noisy labels as the
ground truth limits the accuracy of learning algorithms in the presence of
strong disagreement. This problem is critical for applications in domains such
as medical imaging where both the annotation cost and inter-observer
variability are high. In this work, we present a method for simultaneously
learning the individual annotator model and the underlying true label
distribution, using only noisy observations. Each annotator is modeled by a
confusion matrix that is jointly estimated along with the classifier
predictions. We propose to add a regularization term to the loss function that
encourages convergence to the true annotator confusion matrix. We provide a
theoretical argument as to how the regularization is essential to our approach
both for the case of single annotator and multiple annotators. Despite the
simplicity of the idea, experiments on image classification tasks with both
simulated and real labels show that our method either outperforms or performs
on par with the state-of-the-art methods and is capable of estimating the
skills of annotators even with a single label available per image.Comment: CVPR 2019, code snippets include
Stochastic Filter Groups for Multi-Task CNNs: Learning Specialist and Generalist Convolution Kernels
The performance of multi-task learning in Convolutional Neural Networks
(CNNs) hinges on the design of feature sharing between tasks within the
architecture. The number of possible sharing patterns are combinatorial in the
depth of the network and the number of tasks, and thus hand-crafting an
architecture, purely based on the human intuitions of task relationships can be
time-consuming and suboptimal. In this paper, we present a probabilistic
approach to learning task-specific and shared representations in CNNs for
multi-task learning. Specifically, we propose "stochastic filter groups''
(SFG), a mechanism to assign convolution kernels in each layer to "specialist''
or "generalist'' groups, which are specific to or shared across different
tasks, respectively. The SFG modules determine the connectivity between layers
and the structures of task-specific and shared representations in the network.
We employ variational inference to learn the posterior distribution over the
possible grouping of kernels and network parameters. Experiments demonstrate
that the proposed method generalises across multiple tasks and shows improved
performance over baseline methods.Comment: Accepted for oral presentation at ICCV 201
Uncertainty in multitask learning: joint representations for probabilistic MR-only radiotherapy planning
Multi-task neural network architectures provide a mechanism that jointly
integrates information from distinct sources. It is ideal in the context of
MR-only radiotherapy planning as it can jointly regress a synthetic CT (synCT)
scan and segment organs-at-risk (OAR) from MRI. We propose a probabilistic
multi-task network that estimates: 1) intrinsic uncertainty through a
heteroscedastic noise model for spatially-adaptive task loss weighting and 2)
parameter uncertainty through approximate Bayesian inference. This allows
sampling of multiple segmentations and synCTs that share their network
representation. We test our model on prostate cancer scans and show that it
produces more accurate and consistent synCTs with a better estimation in the
variance of the errors, state of the art results in OAR segmentation and a
methodology for quality assurance in radiotherapy treatment planning.Comment: Early-accept at MICCAI 2018, 8 pages, 4 figure
Disentangling Human Error from the Ground Truth in Segmentation of Medical Images
Recent years have seen increasing use of supervised learning methods for
segmentation tasks. However, the predictive performance of these algorithms
depends on the quality of labels. This problem is particularly pertinent in the
medical image domain, where both the annotation cost and inter-observer
variability are high. In a typical label acquisition process, different human
experts provide their estimates of the 'true' segmentation labels under the
influence of their own biases and competence levels. Treating these noisy
labels blindly as the ground truth limits the performance that automatic
segmentation algorithms can achieve. In this work, we present a method for
jointly learning, from purely noisy observations alone, the reliability of
individual annotators and the true segmentation label distributions, using two
coupled CNNs. The separation of the two is achieved by encouraging the
estimated annotators to be maximally unreliable while achieving high fidelity
with the noisy training data. We first define a toy segmentation dataset based
on MNIST and study the properties of the proposed algorithm. We then
demonstrate the utility of the method on three public medical imaging
segmentation datasets with simulated (when necessary) and real diverse
annotations: 1) MSLSC (multiple-sclerosis lesions); 2) BraTS (brain tumours);
3) LIDC-IDRI (lung abnormalities). In all cases, our method outperforms
competing methods and relevant baselines particularly in cases where the number
of annotations is small and the amount of disagreement is large. The
experiments also show strong ability to capture the complex spatial
characteristics of annotators' mistakes